PMC

Comparison of variability of the normalized data in the three sets of technical replicates from the time course dataset. The density plots show the CVs of all data points (either non-normalized or normalized with the five normalization methods) from each set of the technical replicates (TRC1, TRC2 and TRC3).

Ranks of the normalization methods in the normalized time course dataset. The mean, median and standard deviation of the ranks of the normalization method are defined in Table 1. The bar plots are visual representation of the results shown in Tables 1–4 (the "Mean Rank", "Median Rank" and "Standard Deviation" columns). In each plot, mean ranks are shown in pink, median ranks are in blue, and standard deviations of the ranks are shown as the error bars on top of the "Mean" rank bars.

Comparison of the numbers of differentially expressed genes estimated from the normalized IPF dataset using multiple statistical tests. The x-axis shows the numbers of differentially expressed genes estimated using the following statistical tests: Welch's t-tests without permutation (T-test), Wilcoxon rank sum tests without permutation (Wilcoxon test), Welch's t-tests with permutation (T-test, perm), and Wilcoxon rank sum tests with permutation (Wilcoxon test, perm). The y-axis represents the p-values adjusted using the Benjamini & Hochberg FDR procedure. The red line shows the cut off adjusted p-value of 0.05.

Comparison of the numbers of differentially expressed genes estimated from the normalized time course dataset using multiple statistical tests. The x-axis in each plot shows the days when the rats were treated. The y-axis represents the numbers of differentially expressed genes detected between the control vs. each test group using the following statistical tests: Welch's t-tests without permutation (T-test), Wilcoxon rank sum tests without permutation (Wilcoxon test), Welch's t-tests with permutation (T-test, perm), and Wilcoxon rank sum tests with permutation (Wilcoxon test, perm).

MA plots of two pairs of microarrays in the TRC1 replicate set from the time course dataset. The plots in each row show the results from non-normalized data (row 1) and data normalized with each of the five normalization methods (row 2–6). Columns depict two pairs of microarrays, pair 1 (array 1 vs. array 4, left) and pair 2 (array 4 vs. array 5, right), in the TRC1 replicates that exhibit obvious intensity-dependent differences between the arrays. The yellow line in each plot shows the loess fitting of the entire data in the plot.